San Joaquin's clogged river

The swollen San Joaquin River finally began receding last week, but its brief surge above flood monitor stage rekindled concerns that a far more serious flood is becoming more likely each year.

Why? Tens of thousands of dump truck loads worth of dirt wash down the San Joaquin toward the Delta each year. Scientists have found that much of that dirt, or sediment, is deposited on the bottom of the river as it flattens out between Vernalis and Stockton.

That means the bottom of the river may be rising — perhaps 5 to 10 feet in places, according to one levee engineer.

And if the bottom of the river is rising, that means there is less room in the channel to push flood waters out through the Delta.

Like a clogged pipe, the river could more or less burst.

With a snowpack that is 171 percent of normal, and plenty of time for more storms, it could happen even this year.

“If we get higher flows this winter, we’re going to get a blowout much sooner than we did in 1997,” said Chris Neudeck, a levee engineer from Stockton. More than two-dozen levee breaches occurred on the San Joaquin that year.

“It’s going to get very problematic in short order," he said.

If the river is gradually filling in, the channel elevations used to determine flood stage and gauge the risk to the public may no longer be accurate, he said.

Some areas likely are more susceptible than others. Silt sometimes accumulates around bridges or other structures. While the recent high flows may scour some of the mud away, trees and brush growing within the riverbed itself may stubbornly anchor some of it place.

The issue isn’t limited to the San Joaquin itself. The state Department of Water Resources has estimated that three-fifths of the channels in the San Joaquin watershed cannot convey all the water that their levees were designed to hold.

“It’s gotten pretty bad,” said Manteca farmer Mary Hildebrand, whose late father, engineer Alex Hildebrand, warned for many years that the river was silting up. “We just don’t get those high, scouring flows often enough with all of the dams and the way the system is now.”

That is true particularly on the San Joaquin. Levees on the Sacramento River system were built close together so that water would flow fast enough to scour out old mining debris from the Gold Rush days. The San Joaquin wasn’t designed that way.

Neudeck joins south county farmers and Manteca Mayor Steve DeBrum in suggesting the government consider dredging the lower San Joaquin to remove the accumulated sediment. That’s a strategy the federal government and the Port of Stockton have long used to keep Delta channels clear for navigation.

But dredging raises many complicated issues. It can kill tiny organisms that live in the mud, disrupting the food chain for larger fish. It also can mobilize “nasty stuff” that has been buried for years — such as pesticides or toxic metals, said Jeff Mount, a river scientist with the Public Policy Institute of California.

What’s more, dredging isn’t something you do once and then walk away.

“When you dig a hole in the river, the first thing the river does is try to fill it back in,” he said. “Dredging is absolutely unsustainable.”

The river would need to be studied first to determine how much mud actually has accumulated there, Mount said. It’s unclear when such a study was last done.

While sediment is viewed as a flood threat, scientists say the Delta actually needs more of it.

For millions of years, rivers delivered the dirt that helped form the Central Valley as we know it today. Now much of that dirt is blocked upstream by dams, or kept out of the rivers by levees, and never makes it to the Delta.

That’s a problem for some endangered fish, who need muddy water to hide from predators. It’s also a problem for scientists who would like to restore some of the Delta’s historic wetlands. They need sediment to build tidal marshes high enough that they won't be drowned by rising sea levels.

Benefits aside, the return of high water to the San Joaquin raises new flood worries. Locals say the question is who will do something about it.

A long-term flood control plan for the Central Valley calls for removing sediment from the Yolo and Sacramento bypasses, but not from the San Joaquin. The state has the responsibility under California law to maintain Sacramento River channels only.

That said, Michael Mierzwa, a flood adviser with the Department of Water Resources, called the San Joaquin sediment worries a “very valid concern.” He said the draft flood plan will include a study of how much mud has accumulated in rivers.

Tyler Stalker, a spokesman for the U.S. Army Corps of Engineers, said the agency doesn’t know how much sediment is clogging the San Joaquin, but added dredging “could be an option” if it’s found to be necessary.

— Contact reporter Alex Breitler at (209) 546-8295 or abreitler@recordnet.com. Follow him at recordnet.com/breitlerblog and on Twitter @alexbreitler.